My pet theory is that there is no biological father. Grandma just woke up one morning, decided she wanted to try having a child, and magicked Alyssa into being either by accident or design.
This theory could also explain why Giriko and Luna grew up while Alyssa didn't. If Alyssa is a magical construct born from Grandma's wish to have "a child" then it's entirely possible that Grandma simply forgot to add the whole "becoming an adult" part. That kind of innocent absent mindedness with terrifying implications seems entirely up her alley.
I might not rmb if they ever covered why her size is as such (I think it's just a weird unexplained lack of growth).
But one thing does stick in my mind that I do remember. When Alyssa recalled what her mom told her about parenting, she also implied she gave birth to her. Basically she gets the biological parent idea because she is one, but to her, caring for the child is more important than the blood relation.
I suppose it's possible that Alyssa is not that child. But at the very least her mom had
someone. Less convincing she would want to make a homunculus on top of that. More convincing to me is if there is no biological father and magic covered that part. But I believe she gave birth to her either way.